We investigated the concentrations of over 200 chemicals in the Ithaca water system, including many emerging pollutants of concern. 24-hr composite samples were collected 4 times from 5 different locations (raw drinking water, treated drinking water, wastewater influent, wastewater effluent, and Cayuga Lake). We detected many compounds at all points in the water system in varying concentrations. Pharmaceutical and personal care compounds detected most frequently and in the highest concentrations include caffeine, nicotine, metformin, atrazine, and carbamazepine. Microplastics were also detected in lake samples. Based on the influent data, there was no clear difference in concentrations when college students were in town. Ecological investigations suggest that caffeine can alter fish swimming behavior, but only at higher concentrations than those observed in Cayuga Lake. Pilot studies also suggest that small microplastics (5 μm diameter) may cause increased mortality in Daphnia magna.